[gmx-users] eigenvalues

[Tsjerk Wassenaar]

Hey Tom,

Tough. It seems like two oppositish things: don't use too short parts
to comfort you with the idea that there's no relaxation taking place,
but also discard the first part of the simulation to make sure you cut
on the equilibration. If you try to bring these two in line with each
otherr it sums up to extracting the last, but long enough, chunk of
the trajectory that doesn't give you a high cosine content.

The fact that a lot of people use PCA on (too) short trajectories
reflects that many people don't really understand what it is, and can
and can not do. It's one of these tthings that will always give you
answers, but requires care to yield sensible answers. It's easy to
imagine that many collective motions reported in literature as
reflecting functional mechanics are actually just relaxation from the
starting structure. Then again, e.g. crystal packing forces are most
likely to effect the largest modes, which may well be linked to
functional mechanics, but that should then be stated with the analysis
as an explicit assumption, together with some sort of justification.

Hope it sheds some light.

Cheers,

Tsjerk

On Sun, Jan 11, 2009 at 7:51 PM, TJ Piggot <t.piggot at bristol.ac.uk> wrote:
> So just to make sure i got this correct, when looking at the cosine content
> of the principal components i should look at the whole trajectory? Do i need
> to include the initial relaxation in the first few ns of the production
> simulation?
>
> If there is a high cosine content for the whole trajectory is there anything
> else to be done (if i want to look at the low frequency motions of the
> trajectory) except for simulate for longer (i have a very large system so
> not the favoured option!)?
>
> As you say it seems that lots of people use PCA on short trajectories, even
> of large systems, which to me is confusing
>
> Thanks for any insights you can give
>
> Tom
>
> --On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar
> <tsjerkw at gmail.com> wrote:
>
>> Hi Sanjay,
>>
>> Imagine yourself zig-zagging along a line from one place to another.
>> If you look at you're motion (and the variance), you'll find that if
>> you only look at blocks most of it is explained by the zig-zag and
>> nicely periodic (no cosine content as in Berk Hess' paper). Good, you
>> think. But if you look at the whole travel, the most important
>> contribution is the going from one place to another, and if you look
>> at you're displacement over time with respect to the mean, that will
>> give you half a cosine. The fact that results in a block do not fit a
>> cosine does not take away the fact that you're still in the process of
>> relaxation. I know it's not what you want to hear, but I've seen it
>> happen to a complex of >600 residues, where relaxation took more than
>> 30 ns. I also know that people often do PCA on short time
>> trajectories, but it's not the proper thing to do.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Sat, Jan 10, 2009 at 7:34 AM,  <sanjay23 at iitb.ac.in> wrote:
>>>
>>> Hi Tsjerk,
>>> thanks
>>> actually my protein is quite larg (509 aa).i had divided my trajectory in
>>> different part and according to your suggestion i calculated
>>> cosine-content for all, and find that trajectory from 5to15 ns and
>>> 18to25ns having cosine value very less about 0.03 in both cases(with and
>>> without ligands), while other combination showing higher values (>0.6).so
>>> i think my system is Ist converges around 5ns and maintaining it up to 15
>>> ns after that it may be few conformational fluctuation occurring and
>>> finally it get stabilized from 18to15ns.may that part 15to18ns trajectory
>>> is transition period between to conformational fluctuation. i have also
>>> calculated temp. and pressure during whole simulation and i find that it
>>> is exact Gaussian between 5to25ns.so my confusion is whether i take my
>>> trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25,
>>> but 5to25 showing value of cosine >0.6.
>>>
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
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>
>
>
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623